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At least 37 records · Page 2

RectifHydPlus Data Pipeline

The RectifHydPlus Data Pipeline is an open source and fully reproducible data processing pipeline for creating RectifHydPlus—a dataset of historical monthly net electricity generation for all US hydropower plants (>10MW). The pipeline is coded in R, applying tidyverse libraries and code principles, and using the targets data pipeline framework. All data inputs to the RectifHydPlus Data Pipeline are available from public sources. References to all data inputs, as well as instructions for running the RectifHydPlus Data Pipeline, are available on the GitLab code repository: https://code.ornl.gov/turnersw/rectifhydplus

Turner, SeanWilliam Donald [Oak Ridge National Lab↗

RectifHydPlus Data Pipeline v1.1.0

The RectifHydPlus Data Pipeline is an open source and fully reproducible data processing pipeline for creating RectifHydPlus—a dataset of historical monthly net electricity generation for all US hydropower plants (>10MW). The pipeline is coded in R, applying tidyverse libraries and code principles, and using the targets data pipeline framework. All data inputs to the RectifHydPlus Data Pipeline are available from public sources. References to all data inputs, as well as instructions for running the RectifHydPlus Data Pipeline, are available on the GitLab code repository: https://code.ornl.gov/turnersw/rectifhydplus

Turner, SeanWilliam Donald [Oak Ridge National Lab↗

The SPAN512 mid-latitude pulsar survey at the Nançay Radio Telescope

The large number of ongoing surveys for pulsars and transients at various radio observatories is motivated by the science obtained from these sources. Timing and polarisation analysis of relativistic binaries can place strong constraints on theories of gravity. The observation of a growing number of millisecond pulsars (MSPs) spread over the celestial sphere may allow the detection of a stochastic gravitational wave background arising from supermassive black hole binaries. A more complete sample of young pulsars improves our knowledge of neutron star birth and evolution. Transients such as fast radio bursts can serve to probe the intergalactic medium. The SPAN512 pulsar survey covers intermediate Galactic latitudes using the L-band receiver of the Nançay Radio Telescope (NRT). The survey covers 224 sq. deg. of the sky for a total exposure time of 2200 h. Population syntheses predict the discovery of 3 to 19 new normal pulsars and a few MSPs. We present detailed modelling of the NRT beam with its L-band receiver and its sensitivity which we used to precisely assess the expected survey yield. We used the flexible Pulsar Arecibo L-band Feed Array data processing pipeline to search the 47 TB of SPAN512 data for pulsars and transients. The SPAN512 survey discovered two new MSPs and one new middle-aged pulsar. We focus on the analysis of the 2.4-ms spin period pulsar J2205+6012 for which we also report the detection of gamma-ray pulsations. Its narrow pulse width (35µs at an observing frequency of 2.55 GHz) allows for sub-microsecond timing precision over 8 yr, with exciting prospects for pulsar timing array programs.

79 ASTRONOMY AND ASTROPHYSICS↗

Planck 2018 Results - II. Low Frequency Instrument data processing

We present a final description of the data-processing pipeline for the Planck Low Frequency Instrument (LFI), implemented for the 2018 data release. Several improvements have been made with respect to the previous release, especially in the calibration process and in the correction of instrumental features such as the effects of nonlinearity in the response of the analogue-to-digital converters. We provide a brief pedagogical introduction to the complete pipeline, as well as a detailed description of the important changes implemented. Self-consistency of the pipeline is demonstrated using dedicated simulations and null tests. We present the final version of the LFI full sky maps at 30, 44, and 70 GHz, both in temperature and polarization, together with a refined estimate of the solar dipole and a final assessment of the main LFI instrumental parameters.

79 ASTRONOMY AND ASTROPHYSICS↗

The Fifteenth Data Release of the Sloan Digital Sky Surveys: First Release of MaNGA-derived Quantities, Data Visualization Tools, and Stellar Library

Twenty years have passed since first light for the Sloan Digital Sky Survey (SDSS). Here, we release data taken by the fourth phase of SDSS (SDSS-IV) across its first three years of operation (2014 July-2017 July). This is the third data release for SDSS-IV, and the 15th from SDSS (Data Release Fifteen; DR15). New data come from MaNGA—we release 4824 data cubes, as well as the first stellar spectra in the MaNGA Stellar Library (MaStar), the first set of survey-supported analysis products (e.g., stellar and gas kinematics, emission-line and other maps) from the MaNGA Data Analysis Pipeline, and a new data visualization and access tool we call "Marvin." The next data release, DR16, will include new data from both APOGEE-2 and eBOSS; those surveys release no new data here, but we document updates and corrections to their data processing pipelines. The release is cumulative; it also includes the most recent reductions and calibrations of all data taken by SDSS since first light. In this paper, we describe the location and format of the data and tools and cite technical references describing how it was obtained and processed. The SDSS website (www.sdss.org) has also been updated, providing links to data downloads, tutorials, and examples of data use. Although SDSS-IV will continue to collect astronomical data until 2020, and will be followed by SDSS-V (2020–2025), we end this paper by describing plans to ensure the sustainability of the SDSS data archive for many years beyond the collection of data.

79 ASTRONOMY AND ASTROPHYSICS↗

dbprocessing

dbprocessing is a python framework for automating data processing pipelines. The dbprocessing package uses a configuration file to define the input, intermediate, and output data products for a particular data type as well as the processes that connect those data products. In addition, dbprocessing uses python scripts called inspectors to determine if a particular file matches a configured data product. If a particular data product is found, it is ingested into the dbprocessing database (sqlite3 or postgres) which then triggers all of the chained processes to the final data product. While the framework is written in python, it can run software in any language but may require a “wrapper” to translate the dbprocessing command line arguments to the form expected by the software.

Walker, Andrew↗

NSRDB (National Solar Radiation Database Software) [SWR-23-77]

This repository contains all of the methods for the NSRDB data processing pipeline. The NSRDB is a serially complete collection of hourly and half-hourly values of meteorological data and the three most common measurements of solar radiation: global horizontal, direct normal and diffuse horizontal irradiance.

Benton, Brandon↗

Guiding the choice of informatics software and tools for lipidomics research applications

Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.

59 BASIC BIOLOGICAL SCIENCES↗

The Iterative Processing Framework: A New Paradigm for Automatic Event Building

Abstract In a traditional data-processing pipeline, waveforms are acquired, a detector makes the signal detections (i.e., arrival times, slownesses, and azimuths) and passes them to an associator. The associator then links the detections to the fitting-event hypotheses to generate an event bulletin. Most of the time, this traditional pipeline requires substantial human-analyst involvement to improve the quality of the resulting event bulletin. For the year 2017, for instance, International Data Center (IDC) analysts rejected about 40% of the events in the automatic bulletin and manually built 30% of the legitimate events. Here, we introduce an iterative processing framework (IPF) that includes a new data-processing module that incorporates automatic analyst behaviors (auto analyst [AA]) into the event-building pipeline. In the proposed framework, through an iterative process, the AA takes over many of the tasks traditionally performed by human analysts. These tasks can be grouped into two major processes: (1) evaluating small events with a low number of location-defining arrival phases to improve their formation; and (2) scanning for and exploiting unassociated arrivals to form potential events missed by previous association runs. To test the proposed framework, we processed a two-week period (15–28 May 2010) of the signal-detections dataset from the IDC. Comparison with an expert analyst-reviewed bulletin for the same time period suggests that IPF performs better than the traditional pipelines (IDC and baseline pipelines). The majority of the additional events built by the AA are low-magnitude events that were missed by these traditional pipelines. The AA also adds additional signal detections to existing events, which saves analyst time, even if the event locations are not significantly affected.

58 GEOSCIENCES↗

A Pipeline for Large Data Processing Using Regular Sampling for Unstructured Grids

Large simulation data requires a lot of time and computational resources to compute, store, analyze, visualize, and run user studies. Today, the largest cost of a supercomputer is not hardware but maintenance, in particular energy consumption. Our goal is to balance energy consumption and cognitive value of visualizations of resulting data. This requires us to go through the entire processing pipeline, from simulation to user studies. To reduce the amount of resources, data can be sampled or compressed. While this adds more computation time, the computational overhead is negligible compared to the simulation time. We built a processing pipeline at the example of regular sampling. The reasons for this choice are two-fold: using a simple example reduces unnecessary complexity as we know what to expect from the results. Furthermore, it provides a good baseline for future, more elaborate sampling methods. We measured time and energy for each test we did, and we conducted user studies in Amazon Mechanical Turk (AMT) for a range of different results we produced through sampling.

97 MATHEMATICS AND COMPUTING↗

RTN-117: Image Calibration and Instrument Signal Removal for the First Year of the LSST

The NSF-DOE Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) requires calibration products that provide uniform, stable, and accurate photometric and astrometric performance across the 3.2 gigapixel focal plane and throughout the 10-year survey. This paper details the algorithms and workflows used to produce instrument calibrations and remove instrumental artifacts for Data Preview 2 (DP2)---the first end-to-end processing demonstration using on-sky data with the LSST Camera (LSSTCam). We describe the verification, acceptance, and certification framework used to assess calibration quality and quantify residual systematics. We show baseline metrics on calibrated science images to evaluate the robustness of the calibration and instrument signature removal (ISR) data processing pipelines for DP2. Finally, we summarize the known limitations observed in DP2 production and outline expected algorithmic improvements for the first public LSST data release (Data Release~1, DR1).

79 ASTRONOMY AND ASTROPHYSICS↗

The FRB-searching Pipeline of the Tianlai Cylinder Pathfinder Array

This paper presents the design, calibration, and survey strategy of the Fast Radio Burst (FRB) digital backend and its real-time data processing pipeline employed in the Tianlai Cylinder Pathfinder Array. The array, consisting of three parallel cylindrical reflectors and equipped with 96 dual-polarization feeds, is a radio interferometer array designed for conducting drift scans of the northern celestial semi-sphere. The FRB digital backend enables the formation of 96 digital beams, effectively covering an area of approximately 40 square degrees with the 3 dB beam. Our pipeline demonstrates the capability to conduct an automatic search of FRBs, detecting at quasi-real-time and classifying FRB candidates automatically. The current FRB searching pipeline has an overall recall rate of 88%. During the commissioning phase, we successfully detected signals emitted by four well-known pulsars: PSR B0329+54, B2021+51, B0823+26, and B2020+28. We report the first discovery of an FRB by our array, designated as FRB 20220414A. We also investigate the optimal arrangement for the digitally formed beams to achieve maximum detection rate by numerical simulation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

RectifHyd Version 2.0: Historical and counterfactual-climatological hydropower monthly generation totals for CONUS plants, 1980 – 2019

This dataset will contain the following files: - RectifHydV2.zip – the RectifHydV2 dataset, split into two files: o RectifHydV2_Actual_MWh.csv: Estimated actual monthly net generation from 590 Hydropower Plants (>10MW nameplate) in CONUS, 1980 – 2019 o RectifHydV2_Counterfactual_MWh.csv: Counterfactual (climate-only) monthly net generation from 590 Hydropower Plants (>10MW nameplate) in CONUS, 1980 – 2019 - RectifHydV2_code.zip: Full data processing pipeline, coded using R {targets} framework. This is a snapshot release (v1.0) of the code repository stored at https://code.ornl.gov/turnersw/rectifhydv2 - RectifHydV2_inputs.zip: Complete set of input data used to create RectifHydV2, organized for direct entry into “/data/” directory of the RectifHydV2 reproducible data pipeline - RectifHydV2_misc.zip: - RectifHydV2_dailyRelease.csv

13 HYDRO ENERGY↗

metabCombiner 2.0: Disparate Multi-Dataset Feature Alignment for LC-MS Metabolomics

Liquid chromatography–high-resolution mass spectrometry (LC-HRMS), as applied to untargeted metabolomics, enables the simultaneous detection of thousands of small molecules, generating complex datasets. Alignment is a crucial step in data processing pipelines, whereby LC-MS features derived from common ions are assembled into a unified matrix amenable to further analysis. Variability in the analytical factors that influence liquid chromatography separations complicates data alignment. This is prominent when aligning data acquired in different laboratories, generated using non-identical instruments, or between batches from large-scale studies. Previously, we developed metabCombiner for aligning disparately acquired LC-MS metabolomics datasets. Here, we report significant upgrades to metabCombiner that enable the stepwise alignment of multiple untargeted LC-MS metabolomics datasets, facilitating inter-laboratory reproducibility studies. To accomplish this, a “primary” feature list is used as a template for matching compounds in “target” feature lists. We demonstrate this workflow by aligning four lipidomics datasets from core laboratories generated using each institution’s in-house LC-MS instrumentation and methods. We also introduce batchCombine, an application of the metabCombiner framework for aligning experiments composed of multiple batches. metabCombiner is available as an R package on Github and Bioconductor, along with a new online version implemented as an R Shiny App.

97 MATHEMATICS AND COMPUTING↗

Characterization of contaminants in the Lyman-alpha forest auto-correlation with DESI

Baryon Acoustic Oscillations can be measured with sub-percent precision above redshift two with the Lyman-α (Lyα) forest auto-correlation and its cross-correlation with quasar positions. This is one of the key goals of the Dark Energy Spectroscopic Instrument (DESI) which started its main survey in May 2021. We present in this paper a study of the contaminants to the Lyα forest which are mainly caused by correlated signals introduced by the spectroscopic data processing pipeline as well as astrophysical contaminants due to foreground absorption in the intergalactic medium. Notably, an excess signal caused by the sky background subtraction noise is present in the Lyα auto-correlation in the first line-of-sight separation bin. We use synthetic data to isolate this contribution, we also characterize the effect of spectro-photometric calibration noise, and propose a simple model to account for both effects in the analysis of the Lyα forest. We then measure the auto-correlation of the quasar flux transmission fraction of low redshift quasars, where there is no Lyα forest absorption but only its contaminants. We demonstrate that we can interpret the data with a two-component model: data processing noise and triply ionized Silicon and Carbon auto-correlations. This result can be used to improve the modeling of the Lyα auto-correlation function measured with DESI.

79 ASTRONOMY AND ASTROPHYSICS↗

A Framework for Compressing Unstructured Scientific Data via Serialization

We present a general framework for compressing unstructured scientific data with known local connectivity. A common application is simulation data defined on arbitrary finite element meshes. The framework employs a greedy topology preserving reordering of original nodes which allows for seamless integration into existing data processing pipelines. This reordering process depends solely on mesh connectivity and can be performed offline for optimal efficiency. However, the algorithm’s greedy nature also supports on-the-fly implementation. The proposed method is compatible with any compression algorithm that leverages spatial correlations within the data. The effectiveness of this approach is demonstrated on a large-scale real dataset using several compression methods, including MGARD, SZ, and ZFP.

Reshniak, Viktor [ORNL] (ORCID:0000000315454462)↗

Real-Time Machine Learning Inferencing with Edge Computing Devices from Google and Intel

Machine Learning (ML) has been demonstrated to accelerate discovery and improve the accuracy of many measurements in astrophysics and high energy physics research. As an increasingly commonplace tool, we have reached a new set of challenges in the deployment of ML, at the forefront of which is their computational complexity. The goal of this project is to explore the viability of dedicated machine learning hardware, such as Google’s Coral/Edge TPU and Intel’s Movidius Myriad devices, in astrophysics and high energy physics applications. ML algorithms, while faster than traditional methods, can become the bottleneck in data processing pipelines --- which is a critical issue in systems that require low latency. Within the context of high energy physics and astrophysics, we test this hardware in an attempt to find if it is able to reduce the computational cost of machine learning. We have benchmarked some of these devices, specifically the Google Coral Dev Board and th e Google AIY Vision Kit (Containing Intel’s Movidius Myriad 2).This was done via a strong gravitational lens finding application and a known data set of lenses, simulating a realistic astrophysics application of machine learning, and compare their results to that of traditional computer hardware.

Hawks, Benjamin↗

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data

Background: Metagenomics and metatranscriptomics studies provide valuable insight into the composition and function of microbial populations from diverse environments, however the data processing pipelines that rely on mapping reads to gene catalogs or genome databases for cultured strains yield results that underrepresent the genes and functional potential of uncultured microbes. Recent improvements in sequence assembly methods have eased the reliance on genome databases, thereby allowing the recovery of genomes from uncultured microbes. However, configuring these tools, linking them with advanced binning and annotation tools, and maintaining provenance of the processing continues to be challenging for researchers. Results: Here we present ATLAS, a software package for customizable data processing from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to assemble, annotate, quantify, and bin metagenome and metatranscriptome data. Genome-centric resolution and abundance estimates are provided for each sample in a dataset. ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. Conclusions: ATLAS provides a user-friendly, modular and customizable Snakemake workflow for metagenome and metatranscriptome data processing; it is easily installable with conda and maintained as open-source on GitHub at https://github.com/metagenome-atlas/atlas.

59 BASIC BIOLOGICAL SCIENCES↗